"By making emergency contraception available to women of all ages, the FDA is taking an important step to reduce unintended pregnancies and put women in control of their futures," Hogue said in a statement.
But an opponent of the contraception plan, at the anti-abortion Family Research Council, criticized the government for not sticking with its decision to appeal.
"We're very concerned and disappointed at the same time because what we see here is the government caving to political pressure instead of putting first the health and safety of girls (and) parental rights," said Anna Higgins, director of the council's Center for Human Dignity.
The government had appealed the judge's underlying April 5 ruling, which ordered emergency contraceptives based on the hormone levonorgestrel be made available without a prescription, over the counter and without point-of-sale or age restrictions.
It had asked the judge to suspend the effect of that ruling until the appeals court could decide the case. But the judge declined, saying the government's decision to restrict sales of the morning-after pill was "politically motivated, scientifically unjustified and contrary to agency precedent." He also said there was no basis to deny the request to make the drugs widely available.
The government had argued that "substantial market confusion" could result if the judge's ruling were enforced while appeals were pending, only to be later overturned.
Last week, an appeals court dealt the government a setback by saying it would immediately permit unrestricted sales of the two-pill version of the emergency contraception until the appeal was decided.
The morning-after pill contains a higher dose of the female hormone progestin than is in regular birth control pills. Taking it within 72 hours of rape, condom failure or just forgetting regular contraception can cut the chances of pregnancy by up to 89 percent, but it works best within the first 24 hours. If a girl or woman already is pregnant, the pill, which prevents ovulation or fertilization of an egg, has no effect.